> >Also note that by some conventions, "2OA2" in a PDB file really means
> >atom "OA22".
> >
> I didn't know that. What conventions are those?
Well, PDB atom names are supposed to have the atomic symbol right
justified in the first two columns followed by a remoteness indicator
and then a branching number. However, that isn't a sufficient number of
fields for all situations, such as when significant symmetry is present
in a system, and so a third field is required. This numeric field
occupies the first column when the atom symbol itself is only one
character.
With hydrogens, this first numeric field has the additional defined
purpose of enumerating (NMR?) equivalent hydrogens, so you will see
atoms like "2HD" and "3HD" in ARG for instance.
However, in the Amber world, the atomic symbol always comes first. Thus
a PDB hydrogen 2HH2 becomes HH22 in Amber. Going from PDB to Amber is
easy, but the reverse is not trivial, since Amber "CD1" remains PDB
"CD1", but Amber "HE2" becomes "2HE" and "HH22" becomes "2HH2".
Ambiguity occurs when there is a four-letter atom name which is not a
hydrogen. "OA22" in Amber would thus need to become "2OA2" in order to
comply with the PDB convention of having the Atomic symbol right
justified in the first two columns of the file. However, that
convention is only explicitly enforced for amino acids, so in theory
"OA22" would be legal for a non-amino acid, whereas "2OA2" is required
if the residue is an amino acid.
What a mess!
Cheers,
Warren
--
mailto:warren@...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> >Also note that by some conventions, "2OA2" in a PDB file really means
> >atom "OA22".
> >
> I didn't know that. What conventions are those?
>
> >Furthermore, in your example, they [ATOM IDs] are not unique (a
> mistake?).
> >
> yup, a mistake.
>
> >However, I am trying to bend PyMOL around to meet your needs a bit
> >better.
> >
> >Towards this end, I've created a new setting "pdb_retain_ids" which
> >preserves the original PDB serial numbers in the output file.
> >
> >In future PyMOL versions, so long as
> >
> >set retain_order, 1
> >set pdb_retain_ids, 1
> >set pdb_no_end_record, 1
> >
> That's absolutely fantastic. Right now, I have to use PyMOL, MOE and
> AMBER (sander and carnal are the real problems) on the same systems,
and
> anything that makes this less painful is great! I'll probably set
> retain_order and pdb_retain_ids in my .pymolrc.py and upgrade to the
CVS
> version within the next couple of days.
>
> Thanks!
>
> -michael
> --
> michael lerner
>
>
>
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